Proteomic analyses bring new insights into the effect of a dark stress on lipid biosynthesis in Phaeodactylum tricornutum

Assessment of heavy metals and environmental stress conditions on the production potential of polyunsaturated fatty acids (PUFAs) in indigenous microalgae isolated from the Gulf of Mannar coastal waters

The present study evaluated the effects of heavy metals, viz., lead, mercury, and cadmium, on growth, chlorophyll a, b, c, carotenoids, and PUFA content of marine microalgae Chlorella sp. and Cylindrotheca fusiformis. At 96-h exposure, the IC50 values for Hg2+, Pb2+, and Cd2+ were 0.85 mg/L, 2.4 mg/L, and 5.3 mg/L respectively, in Chlorella sp. In C. fusiformis, IC50 values for Hg2+, Pb2+, and Cd2+ were 0.5 mg/L, 1.2 mg/L, and 3 mg/L respectively. The pigment contents of both microalgae were significantly affected upon heavy metal exposure. In Chlorella sp. and C. fusiformis, the exposed concentrations of Hg2+ averagely decreased the PUFA content by 76.34% and 78.68%, respectively. Similarly, Pb2+-exposed concentrations resulted in 54.50% and 82.64% average reductions in PUFA content of Chlorella sp. and C. fusiformis, respectively. Cd2+-exposed concentrations showed 32.58% and 40.54% average reduction in PUFA content of Chlorella sp. and C. fusiformis, respectively. Among the environmental stress conditions, the dark treatment has increased total PUFA content by 6.63% in Chlorella sp. and 3.92% in C. fusiformis. It was observed that the 50% nitrogen starvation (two-stage) significantly improved the PUFA production from 26.47 ± 6.55% to 40.92 ± 10.74% in Chlorella sp. and from 11.23 ± 5.01 to 32.8 ± 14.17% in C. fusiformis. The toxicity for both microalgae was followed in the order Hg2+ > Pb2+ > Cd2+. Among the two species, Chlorella sp. has shown a high tolerance to heavy metals and can be effectively utilized in PUFA production.

A Coculture of Photoautotrophs and Hydrolytic Heterotrophs Enables Efficient Upcycling of Starch from Wastewater toward Biomass-Derived Products: Synergistic Interactions Impacting Metabolism of the Consortium

Even with particular interest in sustainable development, due to the limited types of bioavailable carbon sources that could support heterotrophic/mixotrophic growth, microalgae-derived products still suffer from inconsistent yield and high costs. This study demonstrates a successful cocultivation of the photoautotroph Chlorella vulgaris with a hydrolytic-enzyme-abundant heterotroph, Saccharomycopsis fibuligera, enabling efficient starch upcycling from water/wastewater toward enhancing microalgae-dominant biomass and lipid production. The enzymatic activities of S. fibuligera contributed to the hydrolysis of starch into glucose, generating a 7-fold higher biomass through mixotrophic/heterotrophic growth of C. vulgaris. Further, scanning transmission electron microscopy (STEM) and quantitative analysis suggested a significantly induced accumulation of lipids in C. vulgaris. Results of meta-transcriptomics revealed the critical regulatory role of illumination in interaction shifting. Gene expression for glycolysis and lipid biosynthesis of C. vulgaris were highly activated during dark periods. Meanwhile, during illumination periods, genes coding for glucoamylase and the sulfur-related activities in S. fibuligera were significantly upregulated, leading to induced starch hydrolysis and potential increased competition for sulfur utilization, respectively. This study indicates that hydrolytic organisms could collaborate to make starch bioavailable for nonhydrolytic microalgae, thus broadening the substrate spectrum and making starch a novel biotechnological feedstock for microalgae-derived products, e.g., biofuels or single-cell protein.

A chlorophyll c synthase widely co-opted by phytoplankton

Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.

The redox state of the plastoquinone (PQ) pool is connected to thylakoid lipid saturation in a marine diatom

The redox state of the plastoquinone (PQ) pool is a known sensor for retrograde signaling. In this paper, we asked, "does the redox state of the PQ pool modulate the saturation state of thylakoid lipids?" Data from fatty acid composition and mRNA transcript abundance analyses suggest a strong connection between these two aspects in a model marine diatom. Fatty acid profiles of Phaeodactylum tricornutum exhibited specific changes when the redox state of the PQ pool was modulated by light and two chemical inhibitors [3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB)]. Data from liquid chromatography with tandem mass spectrometry (LC-MS/MS) indicated a ca. 7-20% decrease in the saturation state of all four conserved thylakoid lipids in response to an oxidized PQ pool. The redox signals generated from an oxidized PQ pool in plastids also increased the mRNA transcript abundance of nuclear-encoded C16 fatty acid desaturases (FADs), with peak upregulation on a timescale of 6 to 12 h. The connection between the redox state of the PQ pool and thylakoid lipid saturation suggests a heretofore unrecognized retrograde signaling pathway that couples photosynthetic electron transport and the physical state of thylakoid membrane lipids.

Dark stress for improved lipid quantity and quality in bioprospected acid-tolerant green microalgae

The cost of microalgae cultivation is one of the largest limitations to achieving sustainable, large-scale microalgae production of commercially desirable lipids. Utilizing CO2 as a 'free' carbon source from waste industrial flue gas emissions can offer wide-ranging cost savings. However, these gas streams typically create acidic environments, in which most microalgae cannot survive due to the concentration of CO2 and the presence of other acidic gasses such as NO2 and SO2. To address this situation, we investigated growth of a mixed acid-tolerant green microalgal culture (91% dominated by a single Coccomyxa sp. taxon) bioprospected at pH 2.8 from an acid mine drainage impacted water body. The culture was grown at pH 2.5 and fed with a simulated flue gas containing 6% CO2 and 94% N2. On reaching the end of the exponential growth phase, the culture was exposed to either continued light-dark cycle conditions or continual dark conditions. After three days in the dark, the biomass consisted of 28% of lipids, which was 42% higher than at the end of the exponential phase and 55% higher than the maximum lipid content achieved under light/dark conditions. The stress caused by being continually in the dark also favoured the production of omega-3 and omega-6 polyunsaturated fatty acids (PUFAs; 19.47% and 21.04%, respectively, after 7 days) compared to 7-days of light-dark treatment (1.94% and 9.53%, respectively) and showed an increase in nitrogen content (C:N ratio of 6.4) compared to light-dark treatment (C:N ratio of 11.9). The results of the research indicate that use of acid tolerant microalgae overcomes issues using flue gasses that will create an acidic environment and that applying dark stress is a low-cost stressor stimulates production of desirable dietary lipids.

Comparative Proteomic Analysis of the Diatom Phaeodactylum tricornutum Reveals New Insights Into Intra- and Extra-Cellular Protein Contents of Its Oval, Fusiform, and Triradiate Morphotypes

Phaeodactylum tricornutum is an atypical diatom since it can display three main morphotypes: fusiform, triradiate, and oval. Such pleomorphism is possible thanks to an original metabolism, which is tightly regulated in order to acclimate to environmental conditions. Currently, studies dedicated to the comparison of each morphotype issued from one specific strain are scarce and little information is available regarding the physiological significance of this morphogenesis. In this study, we performed a comparative proteomic analysis of the three morphotypes from P. tricornutum. Cultures highly enriched in one dominant morphotype (fusiform, triradiate, or oval) of P. tricornutum Pt3 strain were used. Pairwise comparisons highlighted biological processes, which are up- and down-regulated in the oval (e.g., purine and cellular amino acid metabolism) and triradiate morphotypes (e.g., oxido-reduction and glycolytic processes) compared to the fusiform one used as a reference. Intersection analysis allowed us to identify the specific features of the oval morphotype. Results from this study confirmed previous transcriptomic RNA sequencing observation showing that the oval cells present a distinct metabolism with specific protein enrichment compared to fusiform and triradiate cells. Finally, the analysis of the secretome of each morphotype was also performed.

Allelopathy of Alexandrium pacificum on Thalassiosira pseudonana in laboratory cultures

Alexandrium pacificum is a toxin-producing dinoflagellate with allelopathic effects. The elucidation of allelopathic mechanism of A. pacificum is of great significance for understanding A. pacificum blooms. To this end, using the model diatom Thalassiosira pseudonana as a target species, we observed changes in physiological, biochemical and gene transcription of T. pseudonana upon being co-cultured with A. pacificum. We found reciprocal effects between A. pacificum and T. pseudonana, and corroborated A. pacificum's allelopathy on T. pseudonana by observing inhibitory effects of filtrate from A. pacificum culture on the growth of T. pseudonana. We also found that co-culturing with A. pacificum, the expression of T. pseudonana genes related to photosynthesis, oxidative phosphorylation, antioxidant system, nutrient absorption and energy metabolism were drastically influenced. Coupled with the alterations in Fv/Fm (the variable/maximum fluorescence ratio), activity of superoxide dismutase, contents of malondialdehyde, neutral lipid and total protein in T. pseudonana co-cultured with A. pacificum, we propose that A. pacificum allelopathy could reduce the efficiency of photosynthesis and energy metabolism of T. pseudonana and caused the oxidative stress, while the nutrient absorption was also affected by allelopathic effects. The resultant data potentially uncovered the allelopathic molecular mechanism of A. pacificum to model alga T. pseudonana. The changes in nutrient uptake and even energy metabolism in T. pseudonana, as an adaptation to environmental conditions, may prevent it from stress-related injuries. Our finding might advance the understanding of allelopathic mechanism of A. pacificum.

ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum

Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta- and tetraphosphate ((p)ppGpp). In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here, we studied the function of ppGpp in the diatom Phaeodactylum tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using nontargeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.

High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review

Eukaryotic microalgae are a rich source of commercially important metabolites including lipids, pigments, sugars, amino acids and enzymes. However, their inherent genetic potential is usually not enough to support high level production of metabolites of interest. In order to move on from the traditional approach of improving product yields by modification of the cultivation conditions, understanding the metabolic pathways leading to the synthesis of the bioproducts of interest is crucial. Identification of new targets for strain engineering has been greatly facilitated by the rapid development of high-throughput sequencing and spectroscopic techniques discussed in this review. Despite the availability of high throughput analytical tools, examples of gathering and application of proteomic and metabolomic data for metabolic engineering of microalgae are few and mainly limited to lipid production. The present review highlights the application of contemporary proteomic and metabolomic techniques in eukaryotic microalgae for redesigning pathways for enhanced production of algal metabolites.

A brief period of darkness induces changes in fatty acid biosynthesis towards accumulation of saturated fatty acids in Chlorella vulgaris UMT-M1 at stationary growth phase

OBJECTIVE

The effects of a brief (3 days) and prolonged (6 days) period of incubation in darkness and light on the biomass content, lipid content and fatty acid profile in Chlorella vulgaris UMT-M1 were determined.

RESULTS

Three days of incubation in darkness increased saturated fatty acid (SFA) content from 34.0 to 41.4% but decreased monounsaturated fatty acid (MUFA) content from 36.7 to 29.8%. Palmitic acid (C16:0) content was increased from 23.2 to 28.9%, whereas oleic acid (C18:1) content was reduced from 35.4 to 28.8%. Total oil content was slightly decreased from 20.4 to 18.7% after 3 days of darkness, without a significant reduction in biomass compared to 3 days of incubation in light. Biomass and oil content was highest in cultures incubated for 6 days in light, however the stimulatory and inhibitory effects of darkness (or light) on SFA and MUFA content was no longer present at 6 days of incubation.

CONCLUSIONS

Findings from this study suggests that fatty acid composition in C. vulgaris could be modulated to favor either C16:0 or C18:1 by a brief period of either darkness or light incubation, prior to harvesting.

Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application

Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.

Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates

Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.

Two marine natural products, penicillide and verrucarin J, are identified from a chemical genetic screen for neutral lipid accumulation effectors in Phaeodactylum tricornutum

There are a large number of valuable substances in diatoms, such as neutral lipid and pigments. However, due to the lack of clear metabolic pathways, their applications are still limited. Recently, chemical modulators are found to be powerful tools to investigate the metabolic pathways of neutral lipids. Thus, in this study, to identify new neutral lipid accumulation effectors, we screened the natural products that we separated before in the model diatom Phaeodactylum tricornutum (P. tricornutum) by using Nile-red staining method. Two compounds, penicillide and verrucarin J which were isolated from two marine fungal strains, were identified to promote neutral lipid accumulation. However, penicillide and verrucarin J were also found to significantly inhibit the growth of P. tricornutum through specifically inhibiting the photosynthesis of P. tricornutum. Quantitative analysis results showed that penicillide and verrucarin J significantly increased total lipid and triacylglycerol (TAG) contents, which are consistent with previous Nile-red staining results. The expression of key genes such as DGAT2D, GPAT2, LPAT2, and PAP involved in TAG synthesis and unsaturated fatty acids also increased after penicillide and verrucarin J treatments. Besides, many TAG-rich plastoglobuli formed in plastids shown by increased lipid droplets in the cytosol. Finally, penicillide and verrucarin J were found to reduce the expression of synthetic genes of fucoxanthin, and consequently reduced the content of fucoxanthin, indicating that there might be crosstalk between lipid metabolism and fucoxanthin metabolism. Thus, our work exhibits two useful compounds that could be used to further study the metabolic pathways of neutral lipid and fucoxanthin, which will fulfill the promise of diatoms as low cost, high value, sustainable feedstock for high-value products such as neutral lipid and pigments.

Phaeodactylum tricornutum: A Diatom Cell Factory

A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.

Dark metabolism: a molecular insight into how the Antarctic sea-ice diatom Fragilariopsis cylindrus survives long-term darkness

Light underneath Antarctic sea-ice is below detectable limits for up to 4 months of the year. The ability of Antarctic sea-ice diatoms to survive this prolonged darkness relies on their metabolic capability. This study is the first to examine the proteome of a prominent sea-ice diatom in response to extended darkness, focusing on the protein-level mechanisms of dark survival. The Antarctic diatom Fragilariopsis cylindrus was grown under continuous light or darkness for 120 d. The whole cell proteome was quantitatively analysed by nano-LC-MS/MS to investigate metabolic changes that occur during sustained darkness and during recovery under illumination. Enzymes of metabolic pathways, particularly those involved in respiratory processes, tricarboxylic acid cycle, glycolysis, the Entner-Doudoroff pathway, the urea cycle and the mitochondrial electron transport chain became more abundant in the dark. Within the plastid, carbon fixation halted while the upper sections of the glycolysis, gluconeogenesis and pentose phosphate pathways became less active. We have discovered how F. cylindrus utilises an ancient alternative metabolic mechanism that enables its capacity for long-term dark survival. By sustaining essential metabolic processes in the dark, F. cylindrus retains the functionality of the photosynthetic apparatus, ensuring rapid recovery upon re-illumination.

A 2D-DIGE-based proteomic analysis brings new insights into cellular responses of Pseudomonas putida KT2440 during polyhydroxyalkanoates synthesis

Background

Polyhydroxyalkanoates (PHAs) have attracted much attention in recent years as natural alternatives to petroleum-based synthetic polymers that can be broadly used in many applications. Pseudomonas putida KT2440 is a metabolically versatile microorganism that is able to synthesize medium-chain-length PHAs (mcl-PHAs). The phenomena that drive mcl-PHAs synthesis and accumulation seems to be complex and are still poorly understood. Therefore, here we determine new insights into cellular responses of Pseudomonas putida KT2440 during biopolymers production using two-dimensional difference gel-electrophoresis (2D-DIGE) followed by MALDI TOF/TOF mass spectrometry.

Results

The maximum mcl-PHAs content in Pseudomonas putida KT2440 cells was 24% of cell dry weight (CDW) and was triggered by nitrogen depletion. Proteomic analysis allowed the detection of 150 and 131 protein spots differentially regulated at 24 h and 48 h relative to the cell growth stage (8 h), respectively. From those, we successfully identified 84 proteins that had altered expression at 24 h and 74 proteins at 48 h of the mcl-PHAs synthesis process. The protein–protein interactions network indicated that the majority of identified proteins were functionally linkage. The abundance of proteins involved in carbon metabolism were significantly decreased at 24 h and 48 h of the cultivations. Moreover, proteins associated with ATP synthesis were up-regulated suggesting that the enhanced energy metabolism was necessary for the mcl-PHAs accumulation. Furthermore, the induction of proteins involved in nitrogen metabolism, ribosome synthesis and transport was observed. Our results indicate that mcl-PHAs accumulated in the bacterial cells changed the protein abundance involved in stress response and cellular homeostasis.

Conclusions

The presented data allow us to investigate time-course proteome rearrangement in response to nitrogen limitation and biopolyesters accumulation. Our results have pointed out novel proteins that might take part in cellular responses of mcl-PHA-accumulated bacteria. The study provides an additional knowledge that could be helpful to improve the efficiency of the bioprocess and make it more economically feasible.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1146-5) contains supplementary material, which is available to authorized users.

Microalgae biotechnology in Nordic countries - the potential of local strains

Climate change, energy use and food security are the main challenges that our society is facing nowadays. Biofuels and feedstock from microalgae can be part of the solution if high and continuous production is to be ensured. This could be attained in year-round, low cost, outdoor cultivation systems using strains that are not only champion producers of desired compounds but also have robust growth in a dynamic climate. Using microalgae strains adapted to the local conditions may be advantageous particularly in Nordic countries. Here, we review the current status of laboratory and outdoor-scale cultivation in Nordic conditions of local strains for biofuel, high-value compounds and water remediation. Strains suitable for biotechnological purposes were identified from the large and diverse pool represented by saline (NE Atlantic Ocean), brackish (Baltic Sea) and fresh water (lakes and rivers) sources. Energy-efficient annual rotation for cultivation of strains well adapted to Nordic climate has the potential to provide high biomass yields for biotechnological purposes.

Time-Course Proteomic Analysis of Pseudomonas putida KT2440 during Mcl-Polyhydroxyalkanoate Synthesis under Nitrogen Deficiency

Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) have gained great attention as a new green alternative to petrochemical-derived polymers. Due to their outstanding material properties they can be used in a wide range of applications. Pseudomonas putida KT2440 is a metabolically versatile producer of mcl-polyhydroxyalkanoates. Although the metabolism of polyhydroxyalkanoate synthesis by this bacterium has been extensively studied, the comparative proteome analysis from three growth stages of Pseudomonas putida KT2440 cultured with oleic acid during mcl-PHA synthesis has not yet been reported. Therefore; the aim of the study was to compare the proteome of Pseudomonas putida KT2440 at different time points of its cultivation using the 2D difference gel electrophoresis (2D-DIGE) technique. The analyses showed that low levels of a nitrogen source were beneficial for mcl-PHA synthesis. Proteomic analysis revealed that the proteins associated with carbon metabolism were affected by nitrogen starvation and mcl-PHA synthesis. Furthermore, the induction of proteins involved in nitrogen metabolism, ribosome synthesis, and transport was observed, which may be the cellular response to stress related to nitrogen deficiency and mcl-PHA content in bacterial cells. To sum up; this study enabled the investigators to acquire a better knowledge of the molecular mechanisms underlying the induction of polyhydroxyalkanoate synthesis and accumulation in Pseudomonas putida KT2440 that could lead to improved strategies for PHAs in industrial production.

Gibberellin Promotes Cell Growth and Induces Changes in Fatty Acid Biosynthesis and Upregulates Fatty Acid Biosynthetic Genes in Chlorella vulgaris UMT-M1

Microalgae lipids and oils are potential candidates for renewable biofuels and nutritional inventions. Recent studies from our lab have shown that two plant hormones, auxin and jasmonic acid, influence microalgae growth and fatty acid accumulation. Therefore, in this study, a high oil-producing strain Chlorella vulgaris UMT-M1 was selected for hormonal study using gibberellin (GA). Exogenous GA₃ was applied to early stationary culture of C. vulgaris UMT-M1. Results showed that GA₃ gradually increases the cell density of C. vulgaris to up to 42% on days after treatment (DAT)-8 and also capable of delaying the algal senescence. However, the increment in cell density did not enhance the total oil production albeit transient modification of fatty acid compositions was observed for saturated (SFA) and polyunsaturated (PUFA) fatty acids. This illustrates that GA₃ only promotes cell division and growth but not the oil accumulation. In addition, application of GA₃ in culture medium was shown to promote transient increment of palmitic (C16:0) and stearic (C18:0) acids from DAT-4 to DAT-6 and these changes are correlated with the expression of β-ketoacyl ACP synthase I (KAS I) gene.

Comparative proteomic analysis of Ulva prolifera response to high temperature stress

Background

Ulva prolifera belongs to green macroalgae and is the dominant species of green tide. It is distributed worldwide and is therefore subject to high-temperature stress during the growth process. However, the adaptation mechanisms of the response of U. prolifera to high temperatures have not been clearly investigated yet.

Methods

In this study, isobaric tags for relative and absolute quantitation (iTRAQ) labelling was applied in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) to conduct comparative proteomic analysis of the response of U. prolifera to high-temperature stress and to elucidate the involvement of this response in adaptation mechanisms. Differentially expressed proteins (DEPs) of U. prolifera under high temperature (denote UpHT) compared with the control (UpC) were identified. Bioinformatic analyses including GO analysis, pathway analysis, and pathway enrichment analysis was performed to analyse the key metabolic pathways that underlie the thermal tolerance mechanism through protein networks. Quantitative real-time PCR and western blot were performed to validate selected proteins.

Results

In the present study, 1223 DEPs were identified under high temperature compared with the control, which included 790 up-regulated and 433 down-regulated proteins. The high-temperature stimulus mainly induced the expression of glutathione S-transferase, heat shock protein, ascorbate peroxidase, manganese superoxide dismutase, ubiquitin-related protein, lhcSR, rubisco activase, serine/threonine protein kinase 2, adenylate kinase, Ca²⁺-dependent protein kinase (CDPK), disease resistance protein EDS1, metacaspase type II, NDPK2a, 26S proteasome regulatory subunit, ubiquinone oxidoreductase, ATP synthase subunit, SnRK2s, and cytochrome P450. The down-regulated proteins were photosynthesis-related proteins, glutathione reductase, catalase-peroxidase, thioredoxin, thioredoxin peroxidase, PP2C, and carbon fixation-related proteins. Furthermore, biological index analysis indicated that protein content and SOD activity decreased; the value of Fv/Fm dropped to the lowest point after culture for 96 h. However, APX activity and MDA content increased under high temperature.

Conclusion

The present study implied an increase in proteins that were associated with the stress response, oxidative phosphorylation, the cytokinin signal transduction pathway, the abscisic acid signal transduction pathway, and the glutathione metabolism pathway. Proteins that were associated with photosynthesis, carbon fixation in photosynthesis organisms, and the photosynthesis antenna protein pathway were decreased. These pathways played a pivotal role in high temperature regulation. These novel proteins provide a good starting point for further research into their functions using genetic or other approaches. These findings significantly improve the understanding of the molecular mechanisms involved in the tolerance of algae to high-temperature stress.

Electronic supplementary material

The online version of this article (10.1186/s12953-018-0145-5) contains supplementary material, which is available to authorized users.

Transcriptome Profiling of Bigelowiella natans in Response to Light Stress

Bigelowiella natans is a marine chlorarachniophyte whose plastid was acquired secondarily via endosymbiosis with a green alga. During plastid evolution, the photosynthetic endosymbiont would have integrated with the host metabolic pathways. This would require the evolution and coordination of strategies to cope with changes in light intensity that includes changes in the expression of both endosymbiont and host-derived genes. To investigate the transcriptional response to light intensity in chlorarachniophytes, we conducted an RNA-seq experiment to identify differentially expressed genes following a 4-h shift to high or very-low light. A shift to high light altered the expression of over 2,000 genes, many involved with photosynthesis, PSII assembly, primary metabolism, and reactive-oxygen scavenging. These changes are an attempt to optimize photosynthesis and increase energy sinks for excess reductant, while minimizing photooxidative stress. A transfer to very-low light resulted in a lower photosynthetic performance and metabolic alteration, reflecting an energy-limited state. Genes located on the nucleomorph, the vestigial nucleus in the plastid, had few changes in expression in either light treatment, indicating this organelle has relinquished most transcriptional control to the nucleus. Overall, during plastid origin, both host and transferred endosymbiont genes evolved a harmonized transcriptional network to respond to a classic photosynthetic stress.

Changes in the fucoxanthin production and protein profiles in Cylindrotheca closterium in response to blue light-emitting diode light

BACKGROUND

Marine diatoms have a higher fucoxanthin content in comparison to macroalgae. Fucoxanthin features many potent bioactive properties, particularly anti-obesity properties. Despite the great potential for harvesting larger amounts of fucoxanthin, the impacts of light quality (light source, intensity, and photoperiod) on fucoxanthin production and the essential proteins involved in fucoxanthin biosynthesis in marine diatoms remain unclear.

RESULTS

In the present study, Cylindrotheca closterium was selected from four different species of diatoms based on its high fucoxanthin content and productivity. Optimal light conditions (light source, intensity, and regime) were determined by a "Design of Experiment" approach (software MODDE Pro 11 was used). The model indicated that an 18/6 light/darkness regime increased fucoxanthin productivity remarkably as opposed to a 12/12 or 24/0 regime. Eventually, blue light-emitting diode light, as an alternative to fluorescent light, at 100 μmol/m2/s and 18/6 light/darkness regime yielded maximum fucoxanthin productivity and minimal energy consumption. The fucoxanthin production of C. closterium under the predicted optimal light conditions was assessed both in bottle and bag photobioreactors (PBRs). The high fucoxanthin content (25.5 mg/g) obtained from bag PBRs demonstrated the feasibility of large-scale production. The proteomes of C. closterium under the most favorable and unfavorable fucoxanthin biosynthesis light/darkness regimes (18/6 and 24/0, respectively) were compared to identify the essential proteins associated with fucoxanthin accumulation by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. Six proteins that were up-regulated in the 18/6 regime but down-regulated in the 24/0 were identified as important chloroplastic proteins involved in photosynthesis, energy metabolism, and cellular processes.

CONCLUSIONS

Blue light-emitting diode light at 100 μmol/m2/s and 18/6 light/darkness regime induced maximum fucoxanthin productivity in C. closterium and minimized energy consumption. The high fucoxanthin production in the bag photobioreactor under optimal light conditions demonstrated the possibility of commercialization. Proteomics suggests that fucoxanthin biosynthesis is intimately associated with the photosynthetic efficiency of the diatom, providing another technical and bioengineering outlook on fucoxanthin enhancement.

Inhibitory effects of tributyl phosphate on algal growth, photosynthesis, and fatty acid synthesis in the marine diatom Phaeodactylum tricornutum

The widely used solvent extractant, tributyl phosphate (TBP), primarily used as a solvent for the conventional processing of nuclear fuel, has come under scrutiny recently due to concerns surrounding potential environmental contamination and toxicity. In this study, we found that, in Phaeodactylum tricornutum, administration of TBP severely inhibited algal cell growth by reducing photosynthetic efficiency and inducing oxidative stress. We further explored the effect of TBP by examining the gene expression of the photosynthetic electron transport chain and its contribution to reactive oxygen species (ROS) burst. Our data revealed that TBP affected both fatty acid content and profile by regulating the transcription of genes related to glycolysis, fatty acid biosynthesis, and β-oxidation. These results demonstrated that TBP did in fact trigger the synthesis of ROS, disrupting the subcellular membrane structure of this aquatic organism. Our study brings new insight into the fundamental mechanism of toxicity exerted by TBP on the marine alga P. tricornutum.